Index A | B | C | D | E | F | G | I | K | L | M | N | P | Q | R | S | T | U | V A add_substrate() (autoprot.analysis.functional.KSEA method) annotate() (autoprot.analysis.functional.KSEA method) annotate_df() (autoprot.analysis.functional.KSEA method) annotate_phosphosite() (in module autoprot.preprocessing.annotation) auto_run() (autoprot.analysis.clustering.KMeans method) AutoPCA (class in autoprot.analysis.PCA) autoprot.analysis.functional module autoprot.analysis.qc module autoprot.preprocessing.annotation module autoprot.preprocessing.data_handling module autoprot.preprocessing.filtering module autoprot.preprocessing.imputation module autoprot.preprocessing.normalization module autoprot.visualization.annotation module autoprot.visualization.basic module autoprot.visualization.qc module B bar_load() (autoprot.analysis.PCA.AutoPCA method) bi_plot() (autoprot.analysis.PCA.AutoPCA method) boxplot() (in module autoprot.visualization.basic) C charge_plot() (in module autoprot.visualization.qc) cleaning() (in module autoprot.preprocessing.filtering) clear_manual_substrates() (autoprot.analysis.functional.KSEA method) corr_comp() (autoprot.analysis.PCA.AutoPCA method) corr_map() (in module autoprot.visualization.basic) correlogram() (in module autoprot.visualization.basic) count_mod_aa() (in module autoprot.visualization.qc) cyclic_loess() (in module autoprot.preprocessing.normalization) D dima() (in module autoprot.preprocessing.imputation) dimethyl_labeling_efficieny() (in module autoprot.analysis.qc) download_from_ftp() (in module autoprot.preprocessing.data_handling) E enrichment_specificity() (in module autoprot.analysis.qc) F fetch_from_pride() (in module autoprot.preprocessing.data_handling) filter_loc_prob() (in module autoprot.preprocessing.filtering) filter_seq_cov() (in module autoprot.preprocessing.filtering) filter_vv() (in module autoprot.preprocessing.filtering) find_nclusters() (autoprot.analysis.clustering.KMeans method) G get_kinase_overview() (autoprot.analysis.functional.KSEA method) get_subcellular_loc() (in module autoprot.preprocessing.annotation) go_analysis() (in module autoprot.analysis.functional) go_annot() (in module autoprot.preprocessing.annotation) I i_lolli_plot() (in module autoprot.visualization.annotation) i_mirror_lolli_plot() (in module autoprot.visualization.annotation) icharge_plot() (in module autoprot.visualization.qc) icount_mod_aa() (in module autoprot.visualization.qc) ima_plot() (in module autoprot.visualization.basic) imp_median() (in module autoprot.preprocessing.imputation) imp_min_prob() (in module autoprot.preprocessing.imputation) imp_seq() (in module autoprot.preprocessing.imputation) intensity_rank() (in module autoprot.visualization.basic) isequence_logo() (in module autoprot.visualization.annotation) isty_count_plot() (in module autoprot.visualization.qc) ivolcano() (in module autoprot.visualization.basic) K KMeans (class in autoprot.analysis.clustering) KSEA (class in autoprot.analysis.functional) ksea() (autoprot.analysis.functional.KSEA method) L loading_norm() (in module autoprot.preprocessing.normalization) loading_plot() (autoprot.analysis.PCA.AutoPCA method) log_int_plot() (in module autoprot.visualization.basic) M ma_plot() (in module autoprot.visualization.basic) make_cluster() (autoprot.analysis.clustering.KMeans method) mean_sd_plot() (in module autoprot.visualization.basic) miss_analysis() (in module autoprot.analysis.qc) missed_cleavages() (in module autoprot.analysis.qc) module autoprot.analysis.functional autoprot.analysis.qc autoprot.preprocessing.annotation autoprot.preprocessing.data_handling autoprot.preprocessing.filtering autoprot.preprocessing.imputation autoprot.preprocessing.normalization autoprot.visualization.annotation autoprot.visualization.basic autoprot.visualization.qc motif_annot() (in module autoprot.preprocessing.annotation) N norm_to_prot() (in module autoprot.preprocessing.normalization) P pair_plot() (autoprot.analysis.PCA.AutoPCA method) plot_enrichment() (autoprot.analysis.functional.KSEA method) plot_traces() (in module autoprot.visualization.basic) plot_volcano() (autoprot.analysis.functional.KSEA method) prob_plot() (in module autoprot.visualization.basic) ptm_lolli_plot() (in module autoprot.visualization.annotation) ptm_mirror_lolli_plot() (in module autoprot.visualization.annotation) pval_hist() (in module autoprot.visualization.basic) Q quantile_norm() (in module autoprot.preprocessing.normalization) R ratio_plot() (in module autoprot.visualization.basic) read_csv() (in module autoprot.preprocessing.data_handling) remove_non_quant() (in module autoprot.preprocessing.filtering) replot_totals() (autoprot.visualization.basic.UpSetGrouped method) return_enrichment() (autoprot.analysis.functional.KSEA method) return_kinase_substrate() (autoprot.analysis.functional.KSEA method) return_load() (autoprot.analysis.PCA.AutoPCA method) return_score() (autoprot.analysis.PCA.AutoPCA method) S score_plot() (autoprot.analysis.PCA.AutoPCA method) scree() (autoprot.analysis.PCA.AutoPCA method) sequence_logo() (in module autoprot.visualization.annotation) SILAC_labeling_efficiency() (in module autoprot.analysis.qc) sty_count_plot() (in module autoprot.visualization.qc) styling_helper() (autoprot.visualization.basic.UpSetGrouped method) T tmt6plex_labeling_efficiency() (in module autoprot.analysis.qc) to_canonical_ps() (in module autoprot.preprocessing.annotation) to_csv() (in module autoprot.preprocessing.data_handling) U UpSetGrouped (class in autoprot.visualization.basic) V venn_diagram() (in module autoprot.visualization.basic) vis_psites() (in module autoprot.visualization.annotation) volcano() (in module autoprot.visualization.basic) vsn() (in module autoprot.preprocessing.normalization)
